Shear numbers of protein beta-barrels: definition refinements and statistics.
The original definition of shear number for a beta-barrel is not unique if it contains one or more uneven beta-bulges. We define the shear number of a beta-barrel as the minimal change of residue numbers in the backbone direction for all closed paths on the beta-barrel. We also discuss how to overcome some computational difficulties. It is pointed out that some closed beta-sheets should not be considered as beta-barrels. The pertinent statistics obtained from a representative list of the Protein Data Bank entries are summarized. All beta-barrels have positive shear numbers, i.e. they are right-twisted. The shear numbers of most beta-barrels are even, but exceptions do exist. The sizes of beta-ladders in a beta-barrel vary significantly. Most beta-barrels contain uneven beta-bulges, which may have important biological functions.
Liu
W M
WM
Department of Computer and Information Science, Indiana University, Purdue University, Indianapolis 46202-5132, USA.
D000818:Animals; D003627:Data Interpretation, Statistical; D006801:Humans; D008432:Mathematical Computing; D008958:Models, Molecular; D017433:Protein Structure, Secondary; D011506:Proteins / Q000737:chemistry*; D009626:Terminology as Topic
D011506:Proteins